Assemblers that work with Ion Torrent reads

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4.9 years ago

gustavojorge080 ▴ 10

Hello everyone!

I am new at assembling genomes and am looking for assemblers that work well with IonTorrent reads. I just found Spades, Mira and Ray.

Does anyone know anyone else?

Assembly genome gene • 3.0k views

ADD COMMENT • link 4.9 years ago by gustavojorge080 ▴ 10

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The three are good assemblers, and my bet is SPAdes will generate the best assembly. You can add Newbler to the list, if you can get your hands at a copy of it. A very old blog post with some comparisons and suggestions:

First look at Ion Torrent data: De novo assembly

ADD REPLY • link 4.9 years ago by h.mon 35k

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Hello, thank you for answering!

I had read this post and it is very interesting. Unfortunately Newbler is no longer available and CLC and SeqMan are commercial. Fact that left me with nothing.

Anyway, thank you!

ADD REPLY • link 4.9 years ago by gustavojorge080 ▴ 10

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You already have three assemblers, why do you need more?

One problem is Ion Torrent is a niche technology, and its software ecosystem is really scarce.

ADD REPLY • link 4.9 years ago by h.mon 35k

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I need five assemblers for an academic job. And it's very difficult to find assemblers for IonTorrent readings.

ADD REPLY • link 4.9 years ago by gustavojorge080 ▴ 10

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I second spades for this purpose. If you need 5 for some reason look at velvet and soap2denovo as well as Abyss.

Watch out for homopolymers and try to get some Illumina reads (public?) for polishing.

cheers

ADD REPLY • link 4.9 years ago by colindaven 6.3k

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I never used Ion Torrent reads, but you should check if the Torrent Suite provides an assembler.

I need five assemblers for an academic job.

Any assembler that accepts fastq files may be used then, you may just need to convert ubam files to fastq - in case your data is in unaligned bam format. Of course, assemblers not designed to handle the characteristics of Ion Torrent reads will likely do a poor job at assembling them - but who knows, you may even be positively surprised. You may try Minia and MEGAHIT, in addition to the ones you already found and the ones indicated by colindaven .